Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

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TitleForce Field for Peptides and Proteins based on the Classical Drude Oscillator.
Publication TypeJournal Article
Year of Publication2013
AuthorsLopes, PEM, Huang, J, Shim, J, Luo, Y, Li, H, Roux, B, Mackerell, AD
JournalJ Chem Theory Comput
Volume9
Issue12
Pagination5430-5449
Date Published2013 Dec 10
ISSN1549-9626
Abstract

Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1(st) generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S(2) order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion.

DOI10.1021/ct400781b
Alternate JournalJ Chem Theory Comput
PubMed ID24459460
PubMed Central IDPMC3896220
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States